rs7004633

Positions:

• chr8-88748082-A-G
• chr8-88748082-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745653.3(LOC105375630):​n.356-77582A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,036 control chromosomes in the GnomAD database, including 6,764 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6764 hom., cov: 32)
• Consequence: LOC105375630 XR_001745653.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

Genes affected

LOC105375630 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375630	XR_001745653.3	n.356-77582A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649573.1	n.141+47733A>G		intron_variant, non_coding_transcript_variant
	ENST00000653184.1	n.144+47733A>G		intron_variant, non_coding_transcript_variant
	ENST00000659668.1	n.176+47733A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41875 AN: 151918 Hom.: 6731 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.287

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.276 AC: 41960 AN: 152036 Hom.: 6764 Cov.: 32 AF XY: 0.278 AC XY: 20662 AN XY: 74322

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.291

Alfa AF: 0.210 Hom.: 8166

Bravo AF: 0.293

Asia WGS AF: 0.342 AC: 1186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7004633; hg19: chr8-89760311;